In this thesis, phylogenomic and comparative structural analyses of several widespread energy converting enzymes were performed. The focus was on the major subfamilies of the enzymes that process nucleoside triphosphates (ATP and GTP) and on some key enzymes of the electron transfer chains. First, we analyzed the P-loop GTPases, RadA/RecA recombinases, chaperone GroEL, branched-chain α-ketoacid dehydrogenase kinases, chaperone Hsc70, actins, and membrane pyrophosphatases. In the each inspected family we could identify (1) members which were potassium-dependent and/or contained K+ ions in the active site, and (2) potassium-independent enzymes with lysine or arginine residues as catalytic groups that occupy the positions of potassium ions in the homologous, K+-dependent enzymes. Based on the results of our analyses, we suggest that the appearance of the K+-binding sites could precede in evolution the recruitment of positively charged residues (lysine or arginine "fingers") with the latter providing more possibilities to control the enzyme reactions. Second, we have described the distinctive features of a phylogenetically separated subfamily of rotary membrane ATPases which we named N-ATPases. The N-ATPases have a specific operon organization with two additional subunits, absent in other rotary ATPases, and a complete set of Na+-binding ligands in the membrane c-subunits. We made a prediction, which was later confirmed, that these enzymes are capable of Na+ translocation across the membrane and may confer salt tolerance on marine prokaryotes. Third, phylogenomic analysis of the cytochrome bc complexes suggests that these enzyme complexes initially emerged within the bacteria and were then transferred to archaea via lateral gene transfer on several independent occasions. Our analysis indicates that the ancestral form of the cytochrome bc complex was a b6f-type complex; the fusion of the cytochrome b6 and the subunit IV to a "long" cytochrome b of the cytochrome bc1 complexes could have happened in different lineages independently. Fourth, our phylogenomic and comparative structural analyses of the cytochrome bc1 complex and of cytochrome c allowed us to trace how these enzymes became involved in triggering of apoptosis in Metazoa. We could trace the emergence of a specific cardiolipin-binding site within the cytochrome bc complex and the evolution of structural traits that account for the involvement of the cytochrome c as a trigger of apoptosis in vertebrates.

No description available.

Philosophiae Doctor - PhD / The role of phenolic acids in mitigating salt stress tolerance have been well documented. However, there are contradicting reports on the effect of exogenously applied phenolic acids on the growth and development of various plants species. A general trend was observed where phenolic acids were shown to inhibit plant growth and development, with the exception of a few documented cases. One of these such cases is presented in this thesis. This study investigates the role of exogenously applied p-coumaric acid (p-CA) on physio-biochemical and molecular responses of chia seedlings under salt stress. This study is divided into three parts. Part one (Chapter 3) focuses on the impact of exogenous p-coumaric acid on the growth and development of chia seedlings. In this section, chia seedlings were supplemented with exogenous p-CA and the various biochemical and plant growth parameters were measured. The results showed that exogenous p-CA enhanced the growth of chia seedlings. An increase in chlorophyll, proline and superoxide oxide contents were also observed in the p-CA treatment relative to the control. We suggested that the increase in chia seedling growth could possibly be via the activation of reactive oxygen species-signalling pathway involving O2− under the control of proline accumulation (Chapter 3). Given the allopathy, nature of p-coumaric acid it is noteworthy that the response observed in this study may be species dependent, as contrasting responses have been reported in other plant species. Part two (Chapter 4) of this study investigates the influence of piperonylic acid (an inhibitor of endogenous p-coumaric acid) on the growth and development of chia seedlings. In trying to illustrate whether p-CA does play a regulatory role in enhancing pseudocereal plant growth, we treated chia seedlings with the irreversible inhibitor of C4H enzyme, to inhibit the biosynthesis of endogenous p-CA. In this section, chia seedlings were treated with piperonylic acid and changes in plant growth, ROS-induced oxidative damage, p-CA content and antioxidant capacity was monitored. Inhibition of endogenous p-CA restricted chia seedling growth by enhancing ROS-induced oxidative damage as seen for increased levels of superoxide, hydrogen peroxide and the extent of lipid peroxidation. Although an increase in antioxidant activity was observed in response to piperonylic acid, this increase was not sufficient to scavenge the ROS molecules to prevent oxidative damage and ultimate cellular death manifested as reduced plant growth. The results presented in this section support our hypothesis that p-CA play an important regulatory role in enhancing chia seedling growth and development as shown in Chapter 3. Part three (Chapter 5) seeks to identify and functionally characterise p-coumaric acid induced putative protein biomarkers under salt stress conditions in chia seedlings. Previous studies have shown that p-CA reversing the negative effect caused by NaCl-induced salt stress. While these studies were able to demonstrate the involvement of p-CA in promoting plant growth under salt stress conditions, they focussed primarily on the physiological aspect, which lacks in-depth biochemical and molecular analysis (ionomic and proteomic data) which could help in detecting the genes/proteins involved in salt stress tolerance mechanisms. A comparative ionomics and proteomic study was conducted, with the aim of elucidating the pivotal roles of essential macro elements and/or key protein markers involved in p-CA induced salt stress tolerance in chia seedlings. With the exception of Na, all the other macro elements were decreased in the salt treatment. Contrary to what was observed for the salt treatment most of the macro elements were increased in the p-CA treatment. However, the addition of exogenous p-CA to salt stressed seedlings showed an increase in essential macro elements such as Mg and Ca which have been shown to play a key role in plant growth and development. In the proteomic analysis we identified 907 proteins associated with shoots across all treatments. Interestingly, only eight proteins were conserved amongst all treatments. A total of 79 proteins were unique to the p-CA, 26 to the combination treatment (NaCl + p-CA) and only two proteins were unique to the salt stress treatment. The unique proteins identified in each of the treatments were functionally characterised to various subcellular compartments and biological processes. Most of the positively identified proteins were localised to the chloroplast and plays key roles in photosynthesis, transportation, stress responses and signal transduction pathways. Moreover, the protein biomarkers identified in this study (especially in the p-CA treatment) are putative candidates for genetic improvement of salt stress tolerance in plants.

The productivity of agricultural and forest ecosystems in regions at higher latitudes is to a large extent governed by low temperature and moisture conditions. Environmental conditions are acting both above- and below-ground and regulating carbon fluxes and evapotranspiration. However, the understanding of various feedbacks between vegetation and environmental conditions is still unclear. In this thesis, two studies were conducted to understand the physical and biological processes. In the first study, the aim was to simulate soil temperature and moisture dynamics in the bare soil with seasonal frost conditions in China. In the second study, the aims were to model seasonal courses of carbon and evapotranspiration and to examine the responses of photosynthesis, transpiration and respiration on environmental conditions in a boreal Scots pine ecosystem in Finland. In both studies the CoupModel was applied to simulate the dynamic responses of the systems. Both sites represented investigations from which a high number of measurements were available. To understand to what extent the data could be used to increase the understanding of the systems, the Generalized Likelihood Uncertainty Estimation (GLUE) was applied. The GLUE method was useful to reduce basic uncertainties with respect to parameter ranges, model structures and measurements. The strong interactions between soil temperature and moisture processes have indicated by a few behavioral models obtained when constrained by combined temperature and moisture criteria. Model performance on sensible and latent heat fluxes and net ecosystem exchange (NEE) also indicated the coupled processes within the system. Seasonal and diurnal courses were reproduced successfully with reduced parameter ranges. However, uncertainties on what is the most general regulation for transpiration and NEE are still unclear and need further systematic investigations. / QC 20101206

Syftet med denna studie var att utforska hur elever i årskurs 5 utvecklar naturvetenskapliga kunskaper om hur gräs omvandlas till mjölk, där särskilt fokus läggs på sambandet mellan fotosyntes och idisslande djurs matspjälkningssystem. Studiens frågeställningar var följande: Vilka naturvetenskapliga kritiska aspekter behöver elever i årskurs 5 få möjlighet att urskilja för att förstå hur gräs kan omvandlas till mjölk. Hur kan undervisning organiseras för att elever i årskurs 5 ska förstå hur gräs kan omvandlas till mjölk? Denna studie är kvalitativ och har en variationsteoretisk och sociokulturell utgångspunkt. Dessa två teorier presenterar vad undervisningen måste handla om för att skapa bästa förutsättningar till lärande. I denna studie har variationsteorin utgångspunkt i lärandeobjektet, vilka variationsmönster som erbjudits i undervisningen samt de kritiska aspekterna av hur gräs omvandlas till mjölk. Det sociokulturella perspektivet har i denna studie bland annat fokuserat på samspelet mellan eleverna, användning av artefakter och den proximala utvecklingszonen. Resultatet i studien visar att med hjälp av en variationsteoretisk utgångspunkt går det att främja elevers lärande i de naturorienterande ämnen och skapa en variation som bidrar till att elever utvecklar naturvetenskapliga kunskaper om hur gräs omvandlas till mjölk.

La synthèse de l'hydrogène est une alternative viable à l'utilisation du pétrole. Les méthodes telles que l’électrocatalyse font appel à une source d’énergie primaire, ce qui favorise les déchets générés par ces méthodes, de même que le gaspillage d’énergie. Bien qu’ayant de très faibles rendements, les systèmes photocatalytiques permettent la synthèse d’un hydrogène propre et quasi sans déchets. Une perspective permettant d’améliorer encore leur potentiel serait d’éliminer les solvants organiques tels que le DMF, qui sont nocif pour l’environnement et la santé des êtres vivants. Étant donné que le solvant doit être changé, il faut prendre garde à modifier le donneur d’électron sacrificiel et le photosensibilisateur en conséquence. La production de tels solvants est également source de pollution, ce qui atténue le potentiel environnemental de ces méthodes. L’objectif de ce travail est de développer et de tester de nouveaux catalyseurs hydro-solubles variés permettant une amélioration des performances photo-catalytiques actuelles ainsi qu’une performance acceptable dans l’eau. L’étude des propriétés catalytiques est réalisée par l’étude de systèmes homogènes conjugués principalement avec le [Ru(bpy)3]2+ en tant que photosensibilisateur et avec le triethanolamine (dans le DMF) et l’acide ascorbique (dans l’eau) en tant que donneur d’électron sacrificiel. Les catalyseurs présentés lors de ce travail sont des catalyseurs à base de polypyridyl, de cobaloximes et de N-imidoylamidine. Les catalyseurs à base de poly-pyridyl ont d’abord été étudiés puisqu’ils sont réputés pour leur performance en milieux aqueux. La seconde approche consistait à produire des catalyseurs à base de cobaloxime qui aient une performance relativement constante tout d’abord dans les solvants organiques, puis d’adapter ces performances en milieu aqueux. La troisième approche a été de tester des catalyseurs à base de N-imidoylamidine, ce type de catalyseurs n’ayant jamais été testé pour la production d’hydrogène, puis d’en étudier les performances dans l’objectif de paver la voie pour de futures recherches sur le sujet. / The synthesis of hydrogen is a viable alternative to the use of petroleum. Methods such as electrocatalysis use a primary energy source, which reduces the waste generated by these methods, as well as the waste of energy. Although having very low yields, photocatalytic systems allow the synthesis of clean hydrogen with virtually no waste. One prospect to further improve their potential would be to eliminate organic solvents such as DMF, which are harmful to the environment and the health of living beings. Giving the fact that we change the solvent, we need to change the electron sacrificial donor and the photosensitizer as well. The production of such solvents is also a source of pollution, which reduces the environmental potential of these methods. The objective of this work is to develop and test various new water-soluble catalysts allowing an improvement of the current photo-catalytic performances as well as an acceptable performance in water. The study of the catalytic properties is carried out by the study of homogeneous conjugated systems mainly with [Ru(bpy)3]2+ as photosensitizer and with triethanolamine (in DMF) and ascorbic acid (in water) as a sacrificial electron donor. The catalysts presented during this work are catalysts based on polypyridyl, cobaloximes, and N-imidoylamidine. Poly-pyridyl-based catalysts were first studied because they are known for their performance in aqueous media. The second approach was to produce cobaloxime-based catalysts that had relatively constant performance first in organic solvents and then to match this performance in aqueous media. The third approach was to test catalysts based on N-imidoylamidine, as this type of catalyst have never been tested to produce hydrogen, then to study their performance to pave the way for future research on the subject.

No description available.

No description available.

Tesis por compendio / La presente tesis doctoral, titulada "Contribution to the modelling of the light field distribution within Synechocystis sp. PCC 6803 cultures and its influence on cellular photosynthesis processes", engloba diversos trabajos cuyo objetivo es avanzar en la compresión de la distribución lumínica en cultivos de cianobacterias y en los efectos de la luz sobre los mecanismos fotosintéticos de dichos microorganismos. Se trata, en definitiva, de otro paso hacia la integración de modelos matemáticos sobre la fotosíntesis a nivel celular y a escala de cultivo. En primer lugar, para comprender cómo se comporta un cultivo de bacterias fotosintéticas, es fundamental predecir la distribución del campo de luz a lo largo del perfil del biorreactor, tanto a nivel de intensidad total, como respecto a su distribución de flujo de fotones. La distribución de longitudes de onda presente en el medio es importante puesto que muchos procesos de la fotosíntesis están regulados por ciertas longitudes de onda y, por tanto, están modulados por la distribución espectral - el color - de la luz. Aprovechando las propiedades inherentes ópticas del cultivo, se desarrolló un modelo matemático basado en el concepto de campo auto-consistente. Este algoritmo, bautizado en la correspondiente publicación como Auto-consistent Field Approximation Algorithm (AFA), proporciona una predicción del campo lumínico, incluyendo la evolución espectral del mismo a lo largo del camino óptico, para cultivos aclimatados a distintos valores de radiación. Dicha investigación se publicó en la revista Algal Research mediante el artículo titulado "Light distribution and spectral composition within cultures of micro-algae: Quantitative modelling of the light field in photobioreactors", en el que se valida el algoritmo con datos experimentales de dos cepas de estudio de la cianobacteria Synechocystis. Si bien los resultados fueron satisfactorios, el empleo de la ley de Lambert-Beer con un valor constante de atenuación no permite modelizar la parte del campo de luz con menor intensidad, donde el coeficiente de atenuación deja de ser constante y el comportamiento se desvía del exponencial. Por ello, se decidió modelizar el campo de luz con una función que generaliza el caso exponencial mediante el uso de cálculo fraccionario. Se empleó una función de Mittag-Leffler que cumplía con los requisitos formales y ofrecía un ajuste de los datos mejor al obtenido mediante la ley de Lambert-Beer. Como un hallazgo notable, se determinó que el valor de dicho parámetro, que caracteriza la función de Mittag-Leffler, era el mismo para los datos empíricos de las dos cepas estudiadas. Este trabajo se publicó en la contribución llamada "Estimation of the light field inside photosynthetic microorganism cultures through Mittag-Leffler functions at depleted light conditions" en la revista Journal of Quantitative Spectroscopy & Radiative Transfer. Después se procedió a utilizar sendos trabajos de investigación para calcular el campo de luz en un cultivo de Synechocystis y relacionarlo con su productividad máxima. En concreto se ha estudiado, como indicador del rendimiento de la fotosíntesis, la producción de oxígeno y los mecanismos respiratorios asociados a distintas intensidades de luz. Esta investigación está en su fase final y se está ultimando la escritura del artículo para enviarlo a una revista científica próximamente. Dicho manuscrito se titula "Experimental characterisation of Synechocystis sp. PCC 6803 cultures productivity up on light conditions". Finalmente, se está desarrollando una cuarta contribución titulada "Individual pigment contribution to overall in vivo absorption in Synechocystis sp. PCC 6803 cells". Esta investigación estudia la cantidad de luz absorbida por los cromóforos de Synechocystis en función del tipo de iluminación utilizada y calcula la concentración de pigmentos presentes en la célula. / The present doctoral thesis, entitled "Contribution to the modelling of the light field distribution within Synechocystis sp PCC 6803 cultures and its influence on cellular photosynthesis processes", includes several works whose objective is to advance in the understanding of the light distribution in cyanobacterial cultures and in the effects of light on the photosynthetic mechanisms of these microorganisms. It is, ultimately, another step towards the integration of mathematical models on photosynthesis at the cellular level and at the scale of culture. First, to understand how a culture of photosynthetic bacteria behaves, it is essential to predict the distribution of the light field along the bioreactor profile, both at the level of total intensity and with respect to its photon flux distribution. The distribution of wavelengths present in the medium is important since many processes of photosynthesis are regulated by certain wavelengths and are therefore modulated by the spectral distribution - the colour - of the light. Taking advantage of the inherent optical properties of the culture, a mathematical model based on the self-consistent field concept was developed. This algorithm, named in the corresponding publication as Auto-consistent Field Approximation Algorithm (AFA), provides an estimation of the light field, including the spectral evolution thereof along the optical path-length, for acclimated cultures to different radiation values. This research was published in the journal Algal Research through the article entitled "Light distribution and spectral composition within cultures of micro-algae: Quantitative modelling of the light field in photobioreactors", in which the algorithm is validated with experimental data of two strains of study of the cyanobacterium Synechocystis. Although the results were satisfactory, the use of the Lambert-Beer Law with a constant attenuation value, cannot correctly model the part of the light field with less intensity, where the attenuation coefficient ceases to be constant and the behaviour deviates from the exponential. Therefore, it was decided to model the light field with a function that generalizes the exponential case through the use of fractional calculus. A Mittag-Leffler function was used that fulfilled the formal requirements and offered a better data fit than that obtained with the Lambert-Beer law. As a remarkable finding, it was determined that the value of this parameter, which characterises the Mittag-Leffler function, was the same for the empirical data of both studied strains. This work was published in the contribution called "Estimation of the light field in photosynthetic microorganism cultures through Mittag-Leffler functions at depleted light conditions" in the journal Journal of Quantitative Spectroscopy & Radiative Transfer. Thereafter we proceeded to use both research works to calculate the light field within Synechocystis cultures and relate it to its maximum productivity. Specifically, it has been studied, as an indicator of the performance of photosynthesis, the production of oxygen and the associated respiratory mechanisms under different light intensities. This research is in its final phase and the writing of the article is being finalised to submit it to a scientific journal soon. This manuscript is entitled "Experimental characterization of Synechocystis sp. PCC 6803 cultures productivity up on light conditions". Finally, a fourth contribution entitled "Individual pigment contribution to overall in vivo absorption in Synechocystis sp. PCC 6803 cells" is under development. This research studies the amount of light absorbed by Synechocystis chromophores according to the type of employed illumination and calculates the concentration of pigments present in the cell. / La present tesi doctoral, titulada "Contribution to the modelling of the light field distribution within Synechocystis sp. PCC 6803 cultures and its influence on cellular photosynthesis processes", engloba diversos treballs l'objectiu dels quals és avançar en la compressió de la distribució lumínica en cultius de cianobacteris i en els efectes de la llum sobre els mecanismes fotosintètics d'aquests microorganismes. Llavors, es tracta en definitiva d'un altre pas cap a la integració de models matemàtics sobre la fotosíntesi a nivell cel·lular i a escala de cultiu. En primer lloc, per a comprendre com es comporta un cultiu de bacteris fotosintètics, és fonamental predir la distribució del camp de llum al llarg del perfil del bioreactor, tant a nivell d'intensitat total, com pel que fa a la seua distribució de flux de fotons. La distribució de longituds d'ona present en el medi és important ja que molts processos de la fotosíntesi estan regulats per certes longituds d'ona i, per tant, estan modulats per la distribució espectral - el color - de la llum. Aprofitant les propietats inherents òptiques del cultiu, es va desenvolupar un model matemàtic basat en el concepte de camp auto-consistent. Aquest algoritme, batejat en la corresponent publicació com Auto-consistent Field Approximation Algorithm (AFA), proporciona una predicció del camp lumínic, incloent l'evolució espectral del mateix al llarg del camí òptic, per a cultius aclimatats a diferents valors de radiació. Aquesta investigació es va publicar a la revista Algal Research mitjançant l'article titulat "Light distribution and espectral composition within cultures of micro-algae: Quantitative modelling of the light field in photobioreactors", en què es valida l'algoritme amb dades experimentals de dues soques d'estudi de la cianobacteri Synechocystis. Si bé els resultats van ser satisfactoris, l'ús de la llei de Lambert-Beer amb un valor constant d'atenuació no permet modelitzar la part del camp de llum amb menys intensitat, on el coeficient d'atenuació deixa de ser constant i el comportament es desvia del exponencial. Per això, es va decidir modelitzar el camp de llum amb una funció que generalitza el cas exponencial mitjançant l'ús de càlcul fraccionari. Es va emprar una funció de Mittag-Leffler que complia amb els requisits formals i oferia un ajust de les dades millor a l'obtingut mitjançant la llei de Lambert-Beer. Com una troballa notable, es va determinar que el valor d'aquest paràmetre, que caracteritza la funció de Mittag-Leffler, era el mateix per a les dades empíriques de les dues soques estudiades. Aquest treball es va publicar en la contribució anomenada "Estimation of the light field inside Photosynthetic microorganisme cultures through Mittag-Leffler functions at depleted light conditions" a la revista Journal of Quantitative Spectroscopy & Radiative Transfer. Després, es va procedir a utilitzar sengles treballs d'investigació per calcular el camp de llum en un cultiu de Synechocystis i relacionar-lo amb la seua productivitat màxima. En concret s'ha estudiat, com a indicador del rendiment de la fotosíntesi, la producció d'oxigen i els mecanismes respiratoris associats a diferents intensitats de llum. Aquesta investigació està en la seua fase final i s'està ultimant l'escriptura de l'article per enviar-lo a una revista científica pròximament. Dit manuscrit es titula "Experimental characterisation of Synechocystis sp. PCC 6803 cultures productivity up on light conditions". Finalment, s'està desenvolupant una quarta contribució titulada "Individual pigment contribution to overall in vivo absorption in Synechocystis sp. PCC 6803 cells". Aquesta recerca estudia la quantitat de llum absorbida pels cromòfors de Synechocystis en funció del tipus d'il·luminació utilitzada i calcula la concentració de pigments presents en la cèl·lula. / Fuente Herraiz, D. (2018). Contribution to the modelling of the light field distribution within Synechocystis sp. PCC 6803 cultures and its influence on cellular photosynthesis processes [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/106362 / Compendio

Reducing disease and increasing fruit quality in vigorous vineyards with dense canopies is demanding of time and resources; unfortunately, vineyards of this nature are common in humid environments. This study investigated the effectiveness with which vine capacity and water status could be regulated as well as if they related to fruit quality and wine sensory perception. The treatments regulating vine size and water status were under-trellis groundcover, root manipulation, rootstocks, and irrigation. Treatments were arranged in a strip-split-split plot design before the introduction of the irrigation treatment resulted in incomplete replication in each block. Treatment levels were under-trellis cover crop (CC) compared to under-trellis herbicide (Herb); root restriction bags (RBG) compared to no root manipulation (NRM); three compared rootstocks (101-14, 420-A, riparia Gloire); low water stress (LOW) compared to high water stress (HIGH). Vines grown with RBG and CC regulated vegetative growth more so than conventional treatments, resulting in 56% and 23% greater cluster exposure flux availability (CEFA). High water stress (HIGH) and RBG reduced stem water potential and discriminated less against 13C. Vines grown with RBG and CC consistently reduced harvest berry weight by 17 and 6% compared to conventional treatments. Estimated phenolics were consistently increased by RBG and were correlated with berry weight, vine capacity and CEFA. Sensory attributes were significantly distinguishable between wines produced from vines that differed in both vine capacity and water status, amongst other responses. Treatments have been identified that can alter the sensory perception of wines, with the potential to improve wine quality. / Master of Science